NM_007283.7:c.262+26091C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_007283.7(MGLL):​c.262+26091C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.199 in 152,102 control chromosomes in the GnomAD database, including 3,764 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.20 ( 3764 hom., cov: 32)

Consequence

MGLL
NM_007283.7 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.609

Publications

6 publications found
Variant links:
Genes affected
MGLL (HGNC:17038): (monoglyceride lipase) This gene encodes a serine hydrolase of the AB hydrolase superfamily that catalyzes the conversion of monoacylglycerides to free fatty acids and glycerol. The encoded protein plays a critical role in several physiological processes including pain and nociperception through hydrolysis of the endocannabinoid 2-arachidonoylglycerol. Expression of this gene may play a role in cancer tumorigenesis and metastasis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Feb 2012]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
MGLLNM_007283.7 linkc.262+26091C>T intron_variant Intron 3 of 7 ENST00000265052.10 NP_009214.1 Q99685A0A0C4DFN3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
MGLLENST00000265052.10 linkc.262+26091C>T intron_variant Intron 3 of 7 1 NM_007283.7 ENSP00000265052.5 A0A0C4DFN3

Frequencies

GnomAD3 genomes
AF:
0.200
AC:
30328
AN:
151984
Hom.:
3755
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0586
Gnomad AMI
AF:
0.309
Gnomad AMR
AF:
0.265
Gnomad ASJ
AF:
0.316
Gnomad EAS
AF:
0.168
Gnomad SAS
AF:
0.268
Gnomad FIN
AF:
0.277
Gnomad MID
AF:
0.142
Gnomad NFE
AF:
0.249
Gnomad OTH
AF:
0.188
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.199
AC:
30342
AN:
152102
Hom.:
3764
Cov.:
32
AF XY:
0.204
AC XY:
15148
AN XY:
74346
show subpopulations
African (AFR)
AF:
0.0585
AC:
2427
AN:
41504
American (AMR)
AF:
0.266
AC:
4059
AN:
15280
Ashkenazi Jewish (ASJ)
AF:
0.316
AC:
1094
AN:
3464
East Asian (EAS)
AF:
0.167
AC:
867
AN:
5186
South Asian (SAS)
AF:
0.269
AC:
1292
AN:
4808
European-Finnish (FIN)
AF:
0.277
AC:
2928
AN:
10564
Middle Eastern (MID)
AF:
0.139
AC:
41
AN:
294
European-Non Finnish (NFE)
AF:
0.249
AC:
16954
AN:
67974
Other (OTH)
AF:
0.188
AC:
398
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1184
2368
3553
4737
5921
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
326
652
978
1304
1630
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.238
Hom.:
9409
Bravo
AF:
0.189
Asia WGS
AF:
0.217
AC:
754
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
0.78
DANN
Benign
0.77
PhyloP100
-0.61
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs17282181; hg19: chr3-127474541; API